Transcriptome analysis reveals the time of the fourth round of genome duplication in common carp (Cyprinus carpio)

<p>Abstract</p> <p>Background</p> <p>Common carp (<it>Cyprinus carpio</it>) is thought to have undergone one extra round of genome duplication compared to zebrafish. Transcriptome analysis has been used to study the existence and timing of genome duplication in species for which genome sequences are incomplete. Large-scale transcriptome data for the common carp genome should help reveal the timing of the additional duplication event.</p> <p>Results</p> <p>We have sequenced the transcriptome of common carp using 454 pyrosequencing. After assembling the 454 contigs and the published common carp sequences together, we obtained 49,669 contigs and identified genes using homology searches and an ab initio method. We identified 4,651 orthologous pairs between common carp and zebrafish and found 129,984 paralogous pairs within the common carp. An estimation of the synonymous substitution rate in the orthologous pairs indicated that common carp and zebrafish diverged 120 million years ago (MYA). We identified one round of genome duplication in common carp and estimated that it had occurred 5.6 to 11.3 MYA. In zebrafish, no genome duplication event after speciation was observed, suggesting that, compared to zebrafish, common carp had undergone an additional genome duplication event. We annotated the common carp contigs with Gene Ontology terms and KEGG pathways. Compared with zebrafish gene annotations, we found that a set of biological processes and pathways were enriched in common carp.</p> <p>Conclusions</p> <p>The assembled contigs helped us to estimate the time of the fourth-round of genome duplication in common carp. The resource that we have built as part of this study will help advance functional genomics and genome annotation studies in the future.</p

Anti-trypanosomal effect of Malva sylvestris (Malvaceae) extract on a Trypanosoma brucei brucei-infected mouse model of sleeping sickness

Purpose: To evaluate the antitrypanosomal activity of Malva sylvestris (MS) extract in a Trypanosoma brucei brucei-infected  mouse model of sleeping sickness.Methods: Sleeping sickness was induced by the intraperitoneal injection of Trypanosoma brucei brucei infected blood in mice.  Confirmation of parasitaemia was performed by estimating the parasite count in the plasma on the 12th day after inoculation. All the mice were divided into five groups: control group that received neither infection nor treatment; negative control that was  infected with the parasite but did not receive treatment; MS-treated group that receive MS extract (250 and 500 mg/kg, ip) and standard (STD) group that received levamisole (7.5 mg/kg, ip) for 7 days after the development of parasitaemia. A further parasite count was performed in the blood and cerebrospinal fluid (CSF) after the treatment period. Humoral antibody response,  delayed hypersensitivity reaction, and mobilization of leucocytes were determined after the treatment period in SRBC-sensitized mice.Results: The results indicate that treatment with MS significantly decreased body weight and parasite count in the blood and CSF of mice with Trypanosoma brucei brucei-induced sleeping sickness compared with that in the negative control group. There was a significant increase in paw swelling and decrease in secondary antibody in the MS-treated group compared with that in the  negative control group. However, treatment with MS extract also enhanced the mobilization of the total leucocyte count compared with that in the negative control group.Conclusion: The results demonstrate the anti-trypanosomal activity of Malva sylvestris extract via immunomodulation in a  Trypanosoma brucei brucei-infected mouse model of sleeping sickness.Keywords: Malva sylvestris, Trypanosoma brucei brucei, Sleeping sickness, Immunomodulatory activity, Delayed hypersensitivity reactio

A data analysis method for isochronous mass spectrometry using two time-of-flight detectors at CSRe

The concept of isochronous mass spectrometry (IMS) applying two time-of-flight (TOF) detectors originated many years ago at GSI. However, the corresponding method for data analysis has never been discussed in detail. Recently, two TOF detectors have been installed at CSRe and the new working mode of the ring is under test. In this paper, a data analysis method for this mode is introduced and tested with a series of simulations. The results show that the new IMS method can significantly improve mass resolving power via the additional velocity information of stored ions. This improvement is especially important for nuclides with Lorentz factor $\gamma$-value far away from the transition point $\gamma _t$ of the storage ring CSRe.Comment: published in Chinese Physics C Vol. 39, No. 10 (2015) 10620

Radiality of definable sets

In this article we use techniques developed by Hrushovski-Loeser to study certain metric properties of the Berkovich analytification of a finite morphism of smooth connected projective curves. In recent work, M. Temkin proved a radiality statement for the topological ramification locus associated to such finite morphisms. We generalize this result in two directions. We prove a radiality statement for a more general class of sets which we call definable sets. In another direction, we show that the result of Temkin can be obtained in families

MicroRNA-101 inhibits proliferation, migration and invasion of human glioblastoma by targeting SOX9

Glioblastoma multiforme (GBM) is the most common primary malignant tumors originating in the brain parenchyma. At present, GBM patients have a poor prognosis despite the continuous progress in therapeutic technologies including surgery, radiotherapy, photodynamic therapy, and chemotherapy. Recent studies revealed that miR-101 was remarkably down-regulated in kinds of human cancers and was associated with aggressive tumor cell proliferation and stem cell self-renewal. Data also showed that miR-101 was down-regulated in primary glioma samples and cell lines, but the underlying molecular mechanism of the deregulation of miR-101 in glioma remained largely unknown. In this study, we found that miR-101 could inhibit the proliferation and invasion of glioma cells both in vitro and in vivo by directly targeting SOX9 [sex-determining region Y (SRY)-box9 protein]. Silencing of SOX9 exerted similar effects with miR-101 overexpression on glioma cells proliferation and invasion. Quantitative reverse transcription PCR and Western blotting analysis revealed a negative relationship between miR-101 and SOX9 in human glioma U251MG and U87MG cells, and the luciferase assay indicated that miR-101 altered SOX9 expression by directly targeting on 3′UTR. Taken together, our findings suggest that miR-101 regulates glioma proliferation, migration and invasion via directly down-regulating SOX9 both in vitro and in vivo, and miR-101 may be a potential therapeutic target for future glioma treatment

Electroacupuncture alleviates ciliary muscle cell apoptosis in lens-induced myopic guinea pigs through inhibiting the mitochondrial signaling pathway

AIM: To investigate the effect of electroacupuncture (EA) on the mitochondria-dependent apoptotic signaling pathway in the ciliary muscle of guinea pigs with negative lens-induced myopia (LIM). METHODS: Guinea pigs were randomly divided into normal control (NC) group, LIM group, LIM+SHAM acupoint (LIM+SHAM) group, and LIM+EA group. Animals in the NC group received no intervention, while those in other three groups were covered with -6.0 diopter (D) lenses on right eyes. Meanwhile, animals in the LIM+EA group received EA at Hegu (LI4) combined with Taiyang (EX-HN5) acupoints, while those in the LIM+SHAM group were treated at sham points. After treatments for 1, 2, and 4wk, morphological changes in ciliary muscles were observed with hematoxylin and eosin (H&E) staining and nick end labeling (TUNEL), and the expression of the mitochondrial apoptotic signaling pathway-related molecules in ciliary muscles was measured by real-time quantitative polymerase chain reaction (qPCR) and Western blot. Additionally, the adenosine triphosphate (ATP) contents were also determined in ciliary muscles. RESULTS: Axial length increased significantly in the LIM and LIM+SHAM groups and decreased in the LIM+EA group. The ciliary muscle fibers were broken and destroyed in both LIM and LIM+SHAM groups, whereas those in the LIM+EA group improved significantly. TUNEL assay showed the number of apoptotic cells increased in the LIM and LIM+SHAM groups, whereas reduced in the LIM+EA group. ATP contents showed a significant decrease in the LIM and LIM+SHAM groups, whereas increased after EA treatment. Compared with the NC group, the dynamin-related protein 1 (DRP1), Caspase3, and apoptotic protease activator 1 (APAF1) levels were significantly increased in the LIM group and decreased in the LIM+EA group. CONCLUSION: The results provide evidence of EA inhibiting the development of myopia by regulating the mitochondrial apoptotic signaling pathway